I'm contemplating writing about a character with good motivations whose actions would be considered evil.
In short the story would be about a necromancer killing an entire nation so that he can bring order and peace.

My problem is that while I can convey the logic of this, I have no clue how to write this without making him a pure force of evil or writing a fall-to-evil story.

I can't think of any story where you get to follow the "good" guy and see his challenges; you always get the Mr Bond sit down at the end explaining why the bad guy is good.

How would you go about writing a story about a man who has already fallen to "evil" but still portray him as a good guy without sugar coating his plans?

I'm not quite clear whether you want the audience rooting for the protag, or for this to be a more tragic piece (a likable character with good motivations doing evil). Is, say, Dexter along the lines of what you're aiming for?
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Standback♦May 4 '12 at 15:18

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Whoa, whoa. Hold on a minute. Bone to pick. "Evil protagonist" with "good motivations"? Are you saying he's (considered) evil because he has to kill a nation for the greater good? Because that's not definitively evil. This is one of the central questions of Watchmen, if you've ever read it: Is it right to choose the lesser evil?
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AerovistaeMay 5 '12 at 8:00

...I'm just saying let's not act like he's "fallen to evil"...I would say he hasn't.
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AerovistaeMay 5 '12 at 8:01

6 Answers
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Allow me to respectfully disagree with the other answers currently given. It's quite possible to do this, and I think it's a really interesting challenge.

The first thing to remember is that bad guys don't think they're bad. In the usual plot structure, where the POV follows the good protagonists, it's hard to present this fact, but your story is in the POV of the evil necromancer. So you have the opportunity to show us the inside of the evil mind, which can be really compelling. In order to make the reader believe this, try to hit the following points:

What is the necromancer's goal? Ideally, he should have a goal which the modern, non-evil reader can relate to, even if we recoil at his methods. Is he trying to prevent something even more disastrous? Is he trying to be reunited with a lost lover or family member? For comparison, in the last several books of the Wheel of Time Rand came very close to being an outright evil villain, but the reader sticks with him because we know that he's literally responsible for saving creation.

How did the necromancer get to this place? Can the reader identify with and sympathize with the path that brought him to this place? Avoid cliche here, as it's really easy to fall back on "he was abused as a child" or something similar that's been done innumerable times.

What is the necromancer's personality? What if, in person, he's a really nice guy? Maybe he has a great sense of humor or an interesting hobby. Think of Spike in the early seasons of Buffy the Vampire Slayer, who was in theory as nasty as vampires can get, but engendered the viewer's sympathy by being fun-loving and irreverent.

The examples I mentioned above (Rand and Spike) all involve characters who are eventually redeemed, but you don't have to structure your story that way. You can let your necromancer just slide continually deeper into evil, and let the reader experience the conflict of seeing a character that they like and understand become more and more irredeemable.

Edit: probably the best example I can think of from recent media is actually Tony Soprano from The Sopranos, who is very clearly a bad man who gets worse over the course of the series, but who is nonetheless the protagonist. You might consider examining the way that Tony's character is presented and built for examples of how to do this effectively.

1) Does the story have to be from the POV of the necromancer? Or at the least, does the end have to be?

You can show all the necromancer's challenges from the POV of the people of the nation, and its leaders, as they try to defend themselves, and in the epilogue or the denouement, someone (could be a survivor, could be a third party) points out that the necromancer was right after all. Or the leaders of the nation realize that they themselves have been a threat to peace, but they didn't intend to be, and they back down, or allow themselves to be sacrificed. I just read this setup in a C.E. Murphy novel.

2) Read or see Watchmen. Decide if that structure is worth adapting. (I won't spoil it for those who haven't read/seen it.)

The point is portraying the mind of the bad guy. I have watched, read and re-watched watchmen. But it does not do what i want to do. In it everything is reveled at the end and almost instantly the bad guy's result is accepted. I want to show the bad guy formulating on his plans, gather forces and knowledge.
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BorgelMay 4 '12 at 13:13

The way that bad people with good motivations are often shown is by explaining their wrestling with their evil actions. So if you can show that this person has to struggle with the prospect of destroying a nation, and is reluctant to do it despite the good it will bring, you might be part way there.

If his motivations are good, then he will look for other options, he will struggle with the implications. But, because he is also evil, he will then be able to achieve the results without any qualms. And he will have no remorse. Regret that there was no other way, but not remorse.

There are a lot of stories with a "flawed hero", which might help you. In a sense what you seem to be trying is a "flawed villain", which is quite similar.

The problem is your question is too vague. Kill a nation might be evil. Kill a nation to save a planet? Well, that we can get on board with.

Even if we don't like the guy's actions, we can still have sympathy for him. Sons of Anarchy, The Sopranos, The Godfather -- all prove this. Violence in defense of family, for instance.

You avoid making him a "pure force of evil" by making him a real character. Ask yourself what would drive you to do such a terrible thing and you will come up with a fresh answer that we will be excited to read.

These are subjective values that we ascribe to people and actions. As such they are not effective descriptors for a person, real or imagined.

That being said, your necromancer doesn't seem to be a garden-variety bad guy; it seems to me that anyone who would eliminate an entire nation would have to be a super-villain. A super-villain means that his motivations are beyond the self; his motivations are revenge for (what he believes) is a much larger crime. The current justification he uses for his proposed genocide may have nothing to do with the original awful thing -- but that awful thing is writhing and seething below his surface all the time, turning his heart hard and dark and black. And when you combine that darkness with the immense power of a necromancer - that is a formidable foe indeed.

Maybe the necromancer fought in a war that ravaged his nation, so he comes to power during a devastating crisis and blames the nation that won the war for causing the new crisis. But you don't find that out until the climax. Or maybe the reader knows and the protagonist only finds out (or finds the final piece of the back story) at the climax.

So there's your fully functional three dimensional character: A really bad thing happened that he blames the other nation for, ergo it must die for whatever other reason he can justify to himself and others. You don't need a whole fall-to-evil story. You can and should reveal bits of it either in a prologue, or a lengthy monologue or sprinkled around your story like Easter eggs on a spring Sunday morning. Whatever works for your story.

One of Brandon Sanderson's works explores this idea. I will mark the rest of the answer with a spoiler tag because the relevance to this question is not immediately apparent, and just knowing that it was would be a spoiler.

The title so you can decide if you want to read further:

Mistborn

The relevance:

The heroes oppose a ruler who is ruthless and cruel. They attribute his actions to evil and set out to defeat him and end his reign. When they succeed they discover that his motivations had merit, and by defeating him they have set into motion events which they must now struggle against to prevent a terrible disaster. Over the next two books of the series you gain some sympathy for the ruler as you discover the method behind his madness. You see the heroes cause death and destruction on a scale far beyond the events that led them to act in the first place. You are still sympathetic to them because you have seen how they struggled to make the right choices but made terrible mistakes and caused great suffering.

On the note of Sanderson's works, his novel Elantris explores an evil antagonist with good motivations. He switches to the antagonist's point of view every third chapter, so in a way you could call him a protagonist. He pulls it off so well that this guy is the most interesting character of the lot, imho.
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LexiMay 23 '12 at 4:15